def _apply_tile_transform(tile, contours):
# assuming there's a single transform for the tile
assert (len(tile.transforms) == 1)
transform = tile.transforms[0]
if DEBUG_NO_TRANSFOM:
from rh_renderer import models
transform = models.AffineModel()
out_contours = np.empty_like(contours)
for cnt_idx, cnt in enumerate(contours):
cnt_pts = cnt.reshape((len(cnt), 2))
cnt_pts_transformed = transform.apply(cnt_pts)
cnt_pts_transformed = cnt_pts_transformed.reshape(
(len(cnt_pts_transformed), 1, 2))
out_contours[cnt_idx] = cnt_pts_transformed
return out_contours
# Renders a given tilespec in 1/4 resolution
from __future__ import print_function
import pylab
from rh_renderer.tilespec_renderer import TilespecRenderer
import numpy as np
import time
import json
from rh_renderer import models
if __name__ == '__main__':
ts_fname = 'tilespec_1tile.json'
with open(ts_fname, 'r') as data:
tilespec = json.load(data)
# Create the tilespec renderer
renderer1 = TilespecRenderer(tilespec)
downsample = models.AffineModel(
np.array([[0.25, 0., 0.], [0., 0.25, 0.], [0., 0., 1.]]))
renderer1.add_transformation(downsample)
start_time = time.time()
img1, start_point1 = renderer1.render()
print("Start point is at:", start_point1, "image shape:", img1.shape,
"took: {} seconds".format(time.time() - start_time))
pylab.figure()
pylab.imshow(img1, cmap='gray', vmin=0., vmax=255.)
pylab.show()
def render_tilespec(tile_fname,
output,
scale,
output_type,
in_bbox,
tile_size,
invert_image,
threads_num=1,
empty_placeholder=False,
hist_adjuster_alg_type=None,
from_to_cols_rows=None,
blend_type=BlendType.MULTI_BAND_SEAM):
"""Renders a given tilespec.
If the in_bbox to_x/to_y values are -1, uses the tilespecs to determine the output size.
If tile_size is 0, the output will be a single image, otherwise multiple tiles will be created.
output is either a single filename to save the output in (using the output_type),
or a prefix for the tiles output, which will be of the form: {prefix}_tr%d-tc%d.{output_type}
and the row (tr) and column (tc) values will be one-based."""
start_time = time.time()
# Determine the output shape
if in_bbox[1] == -1 or in_bbox[3] == -1:
image_bbox = common.read_bboxes_grep(tile_fname)
image_bbox[0] = max(image_bbox[0], in_bbox[0])
image_bbox[2] = max(image_bbox[2], in_bbox[2])
if in_bbox[1] > 0:
image_bbox[1] = in_bbox[1]
if in_bbox[3] > 0:
image_bbox[3] = in_bbox[3]
else:
image_bbox = in_bbox
scaled_bbox = [
int(math.floor(image_bbox[0] * scale)),
int(math.ceil(image_bbox[1] * scale)),
int(math.floor(image_bbox[2] * scale)),
int(math.ceil(image_bbox[3] * scale))
]
# Set the post-scale out shape of the image
out_shape = (scaled_bbox[1] - scaled_bbox[0],
scaled_bbox[3] - scaled_bbox[2])
print("Final out_shape for the image: {}".format(out_shape))
hist_adjuster = None
# if hist_adjuster_fname is not None:
# #reference_histogram = HistMatcher(histogram_fname=reference_histogram_fname, saturate_low_pct=0.001, saturate_high_pct=0.001)
# #reference_histogram = HistMatcher(histogram_fname=reference_histogram_fname)
# hist_adjuster = rh_renderer.normalization.hist_adjuster.load_adjuster(hist_adjuster_fname)
# elif hist_adjuster_alg_type is not None:
# if hist_adjuster_alg_type.upper() == 'CLAHE':
# hist_adjuster = HistogramCLAHE()
if hist_adjuster_alg_type is not None:
if hist_adjuster_alg_type.upper() == 'CLAHE':
hist_adjuster = HistogramCLAHE()
if hist_adjuster_alg_type.upper() == 'GB11CLAHE':
hist_adjuster = HistogramGB11CLAHE()
with open(tile_fname, 'r') as data:
tilespec = ujson.load(data)
renderer = TilespecRenderer(tilespec,
hist_adjuster=hist_adjuster,
dynamic=(scale != 1.0),
blend_type=blend_type)
# FOR THE IARPA latest dataset
# trans_model = models.AffineModel(np.array([
# [1., 0., 13679.],
# [0., 1., 2108.],
# [0., 0., 1.]
# ]))
# renderer.add_transformation(trans_model)
# Add the downsampling transformation
if scale != 1.0:
downsample = models.AffineModel(
np.array([[scale, 0., 0.], [0., scale, 0.], [0., 0., 1.]]))
renderer.add_transformation(downsample)
# FOR THE IARPA R2B1 first dataset
# rot = 0.29441193975
# rot_model = models.AffineModel(np.array([
# [math.cos(rot), -math.sin(rot), 0.],
# [math.sin(rot), math.cos(rot), 0.],
# [0., 0., 1.]
# ]))
# renderer.add_transformation(rot_model)
# # FOR THE IARPA R2B1 Layers_1_2 dataset
# rot = 0.3490658504
# rot_model = models.AffineModel(np.array([
# [math.cos(rot), -math.sin(rot), 0.],
# [math.sin(rot), math.cos(rot), 0.],
# [0., 0., 1.]
# ]))
# renderer.add_transformation(rot_model)
if tile_size == 0:
# no tiles, just render a single file
out_fname = "{}.{}".format(os.path.splitext(output)[0], output_type)
out_fname_empty = "{}_empty".format(out_fname)
# Render the image
img, start_point = renderer.crop(scaled_bbox[0], scaled_bbox[2],
scaled_bbox[1] - 1,
scaled_bbox[3] - 1)
print("Rendered cropped and downsampled version")
if empty_placeholder:
if img is None or np.all(img == 0):
# create the empty file, and return
print("saving empty image {}".format(out_fname_empty))
open(out_fname_empty, 'a').close()
print("Rendering and saving empty file {} took {} seconds.".
format(out_fname_empty,
time.time() - start_time))
return
if img is None:
# No actual image, set a blank image of the wanted size
img = np.zeros((out_shape[1], out_shape1[0]), dtype=np.uint8)
start_point = (0, 0)
print("Padding image")
img = pad_image(img, scaled_bbox[0], scaled_bbox[2], start_point)
if invert_image:
print("inverting image")
img = 255 - img
print("saving image {}".format(out_fname))
cv2.imwrite(out_fname, img)
else:
# Tile the image
rows = int(math.ceil(out_shape[1] / float(tile_size)))
cols = int(math.ceil(out_shape[0] / float(tile_size)))
from_row = 0
from_col = 0
to_row = rows
to_col = cols
if from_to_cols_rows is not None:
from_col, from_row, to_col, to_row = from_to_cols_rows
# Iterate over each row and column and save the tile
for cur_row in range(from_row, to_row):
from_y = scaled_bbox[2] + cur_row * tile_size
to_y = min(scaled_bbox[2] + (cur_row + 1) * tile_size,
scaled_bbox[3])
for cur_col in range(from_col, to_col):
tile_start_time = time.time()
out_fname = "{}_tr{}-tc{}.{}".format(output, str(cur_row + 1),
str(cur_col + 1),
output_type)
out_fname_empty = "{}_empty".format(out_fname)
from_x = scaled_bbox[0] + cur_col * tile_size
to_x = min(scaled_bbox[0] + (cur_col + 1) * tile_size,
scaled_bbox[1])
# Render the tile
img, start_point = renderer.crop(from_x, from_y, to_x - 1,
to_y - 1)
print("Rendered cropped and downsampled version")
if empty_placeholder:
if img is None or np.all(img == 0):
# create the empty file, and return
print("saving empty image {}".format(out_fname_empty))
open(out_fname_empty, 'a').close()
continue
if img is None:
# No actual image, set a blank image of the wanted size
img = np.zeros((to_y - from_y, to_x - from_x),
dtype=np.uint8)
start_point = (from_y, from_x)
print("Padding image")
img = pad_image(img, from_x, from_y, start_point)
if invert_image:
print("inverting image")
img = 255 - img
print("saving image {}".format(out_fname))
cv2.imwrite(out_fname, img)
print(
"single tile rendering and saving to {} took {} seconds.".
format(out_fname,
time.time() - tile_start_time))
print("Rendering and saving {} took {} seconds.".format(
tile_fname,
time.time() - start_time))
def render_tilespec(tile_fname, output, scale, output_type, in_bbox, tile_size, invert_image, threads_num=1, empty_placeholder=False, reference_histogram_fname=None, from_to_cols_rows=None):
"""Renders a given tilespec.
If the in_bbox to_x/to_y values are -1, uses the tilespecs to determine the output size.
If tile_size is 0, the output will be a single image, otherwise multiple tiles will be created.
output is either a single filename to save the output in (using the output_type),
or a prefix for the tiles output, which will be of the form: {prefix}_tr%d-tc%d.{output_type}
and the row (tr) and column (tc) values will be one-based."""
start_time = time.time()
# Determine the output shape
if in_bbox[1] == -1 or in_bbox[3] == -1:
image_bbox = BoundingBox.read_bbox_grep(tile_fname)
image_bbox.from_x = max(image_bbox.from_x, in_bbox[0])
image_bbox.from_y = max(image_bbox.from_y, in_bbox[2])
if in_bbox[1] > 0:
image_bbox.to_x = in_bbox[1]
if in_bbox[3] > 0:
image_bbox.to_y = in_bbox[3]
else:
image_bbox = BoundingBox.fromList(in_bbox)
scaled_bbox = BoundingBox(
int(math.floor(image_bbox.from_x * scale)),
int(math.ceil(image_bbox.to_x * scale)),
int(math.floor(image_bbox.from_y * scale)),
int(math.ceil(image_bbox.to_y * scale))
)
# Set the post-scale out shape of the image
out_shape = (scaled_bbox.to_x - scaled_bbox.from_x, scaled_bbox.to_y - scaled_bbox.from_y)
print "Final out_shape for the image: {}".format(out_shape)
reference_histogram = None
if reference_histogram_fname is not None:
#reference_histogram = HistMatcher(histogram_fname=reference_histogram_fname, saturate_low_pct=0.001, saturate_high_pct=0.001)
reference_histogram = HistMatcher(histogram_fname=reference_histogram_fname)
with open(tile_fname, 'r') as data:
tilespec = json.load(data)
renderer = TilespecRenderer(tilespec, hist_adjuster=reference_histogram)
# Add the downsampling transformation
downsample = models.AffineModel(np.array([
[scale, 0., 0.],
[0., scale, 0.],
[0., 0., 1.]
]))
renderer.add_transformation(downsample)
if tile_size == 0:
# no tiles, just render a single file
out_fname = "{}.{}".format(os.path.splitext(output)[0], output_type)
out_fname_empty = "{}_empty".format(out_fname)
# Render the image
img, start_point = renderer.crop(scaled_bbox.from_x, scaled_bbox.from_y, scaled_bbox.to_x - 1, scaled_bbox.to_y - 1)
print "Rendered cropped and downsampled version"
if empty_placeholder:
if img is None or np.all(img == 0):
# create the empty file, and return
print "saving empty image {}".format(out_fname_empty)
open(out_fname_empty, 'a').close()
print "Rendering and saving empty file {} took {} seconds.".format(out_fname_empty, time.time() - start_time)
return
if img is None:
# No actual image, set a blank image of the wanted size
img = np.zeros((out_shape[1], out_shape[0]), dtype=np.uint8)
start_point = (0, 0)
print "Padding image"
img = pad_image(img, scaled_bbox.from_x, scaled_bbox.from_y, start_point)
if invert_image:
print "inverting image"
img = 255 - img
print "saving image {}".format(out_fname)
cv2.imwrite(out_fname, img)
else:
# Tile the image
rows = int(math.ceil(out_shape[1] / float(tile_size)))
cols = int(math.ceil(out_shape[0] / float(tile_size)))
from_row = 0
from_col = 0
to_row = rows
to_col = cols
if from_to_cols_rows is not None:
from_col, from_row, to_col, to_row = from_to_cols_rows
# Iterate over each row and column and save the tile
for cur_row in range(from_row, to_row):
from_y = scaled_bbox.from_y + cur_row * tile_size
to_y = min(scaled_bbox.from_y + (cur_row + 1) * tile_size, scaled_bbox.to_y)
for cur_col in range(from_col, to_col):
tile_start_time = time.time()
out_fname = "{}_tr{}-tc{}.{}".format(output, str(cur_row + 1), str(cur_col + 1), output_type)
out_fname_empty = "{}_empty".format(out_fname)
from_x = scaled_bbox.from_x + cur_col * tile_size
to_x = min(scaled_bbox.from_x + (cur_col + 1) * tile_size, scaled_bbox.to_x)
# Render the tile
img, start_point = renderer.crop(from_x, from_y, to_x - 1, to_y - 1)
print "Rendered cropped and downsampled version"
if empty_placeholder:
if img is None or np.all(img == 0):
# create the empty file, and return
print "saving empty image {}".format(out_fname_empty)
open(out_fname_empty, 'a').close()
continue
if img is None:
# No actual image, set a blank image of the wanted size
img = np.zeros((to_y - from_y, to_x - from_x), dtype=np.uint8)
start_point = (from_y, from_x)
print "Padding image"
img = pad_image(img, from_x, from_y, start_point)
if invert_image:
print "inverting image"
img = 255 - img
print "saving image {}".format(out_fname)
cv2.imwrite(out_fname, img)
print "single tile rendering and saving to {} took {} seconds.".format(out_fname, time.time() - tile_start_time)
print "Rendering and saving {} took {} seconds.".format(tile_fname, time.time() - start_time)
def inverse_transform(model):
mat = model.get_matrix()
new_model = models.AffineModel(np.linalg.inv(mat))
return new_model
def match_and_filter(self, features_kps1, features_descs1, features_kps2,
features_descs2):
match_points = self.match(features_kps1, features_descs1,
features_kps2, features_descs2)
if match_points is None:
return None, None
model, filtered_matches, mask = ransac.filter_matches(
match_points,
match_points,
self._params['model_index'],
self._params['iterations'],
self._params['max_epsilon'],
self._params['min_inlier_ratio'],
self._params['min_num_inlier'],
self._params['max_trust'],
self._params['det_delta'],
self._params['max_stretch'],
self._params['max_rot_deg'],
robust_filter=not self._params['avoid_robust_filter'],
max_distance=self._params['max_distance'])
if model is None:
return None, None
if self._params["use_regularizer"]:
regularizer_model, _, _ = ransac.filter_matches(
match_points,
match_points,
self._params['regularizer_model_index'],
self._params['iterations'],
self._params['max_epsilon'],
self._params['min_inlier_ratio'],
self._params['min_num_inlier'],
self._params['max_trust'],
self._params['det_delta'],
self._params['max_stretch'],
self._params['max_rot_deg'],
robust_filter=not self._params['avoid_robust_filter'],
max_distance=self._params['max_distance'])
if regularizer_model is None:
return None, None
result = model.get_matrix() * (
1 - self._params["regularizer_lambda"]
) + regularizer_model.get_matrix(
) * self._params["regularizer_lambda"]
model = models.AffineModel(result)
if self._params['best_k_matches'] > 0 and self._params[
'best_k_matches'] < len(filtered_matches[0]):
# Only keep the best K matches out of the filtered matches
best_k_matches_idxs = np.argpartition(
match_points[2][mask], -self._params['best_k_matches']
)[-self._params['best_k_matches']:]
filtered_matches = np.array([
match_points[0][mask][best_k_matches_idxs],
match_points[1][mask][best_k_matches_idxs]
])
return model, filtered_matches